Merge pull request #34 from embodied-computation-group/dev

v0.2.2

Author: Nicolas Legrand

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
     - id: isort
       files: ^systole/
 -   repo: https://github.com/ambv/black
-    rev: 21.9b0
+    rev: 21.12b0
     hooks:
     - id: black
       language_version: python3
@@ -16,7 +16,7 @@ repos:
     - id: flake8
       files: ^systole/
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.910'  # Use the sha / tag you want to point at
+    rev: 'v0.920'  # Use the sha / tag you want to point at
     hooks:
     - id: mypy 
       files: ^systole/

.travis.yml

@@ -8,9 +8,6 @@
 .. image:: https://zenodo.org/badge/219720901.svg
    :target: https://zenodo.org/badge/latestdoi/219720901
 
-.. image:: https://travis-ci.org/embodied-computation-group/systole.svg?branch=master
-   :target: https://travis-ci.org/embodied-computation-group/systole
-
 .. image:: https://codecov.io/gh/embodied-computation-group/systole/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/embodied-computation-group/systole
 
@@ -66,6 +63,7 @@ The following packages are required to use Systole:
 * `pyserial <https://pyserial.readthedocs.io/en/latest/pyserial.html>`_ (>=3.4)
 * `setuptools <https://setuptools.pypa.io/en/latest/>`_ (>=38.4)
 * `requests <https://docs.python-requests.org/en/latest/>`_ (>=2.26.0)
+* `tabulate <https://github.com/astanin/python-tabulate/>`_ (>=0.8.9)
 
 
 The Python version should be 3.7 or higher.
@@ -78,6 +76,7 @@ For an introduction to Systole and cardiac signal analysis, you can refer to the
 .. list-table::
    :widths: 60 40
    :header-rows: 0
+   :align: center
 
    * - Cardiac signal analysis 
      - |Colab badge 1|
@@ -157,11 +156,11 @@ Systole implements time-domain, frequency-domain and non-linear HRV indices, as
 .. code-block:: python
 
   from bokeh.layouts import row
-  from systole.plots import plot_frequency, plot_pointcare
+  from systole.plots import plot_frequency, plot_poincare
 
   row(
       plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(300, 200)),
-      plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
+      plot_poincare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
       )
 
 .. image:: https://github.com/embodied-computation-group/systole/blob/dev/source/images/hrv.png

README.rst

@@ -11,4 +11,5 @@ numba>=0.51.2
 tqdm
 requests>=2.24.0
 papermill>=2.2.2
-pytest
+pytest
+tabulate>=0.8.9

requirements-test.txt

@@ -9,4 +9,5 @@ setuptools>=38.4
 packaging
 numba>=0.51.2
 tqdm
-requests>=2.26.0
+requests>=2.26.0
+tabulate>=0.8.9

requirements.txt

@@ -20,7 +20,7 @@ def get_requirements():
 DISTNAME = "systole"
 MAINTAINER = "Nicolas Legrand"
 MAINTAINER_EMAIL = "[email protected]"
-VERSION = "0.2.1"
+VERSION = "0.2.2"
 
 
 if __name__ == "__main__":

setup.py

@@ -6,7 +6,7 @@ Functions
 =========
 
 .. contents:: Table of Contents
-   :depth: 3
+   :depth: 2
 
 Correction
 ----------
@@ -37,6 +37,7 @@ Detection
 
     ppg_peaks
     ecg_peaks
+    res_peaks
     rr_artefacts
     interpolate_clipping
 
@@ -54,8 +55,13 @@ Heart Rate Variability
     pnnX
     rmssd
     time_domain
+    psd
     frequency_domain
-    nonlinear
+    nonlinear_domain
+    poincare
+    recurrence
+    recurrence_matrix
+    all_domain
 
 Plots
 -----
@@ -72,7 +78,7 @@ Plots
     plot_events
     plot_evoked
     plot_frequency
-    plot_pointcare
+    plot_poincare
     plot_raw
     plot_rr
     plot_shortlong